Connecting the components in the schematic

Connect +5 VCC

Open Schematic Layout Editor
Select Place Wire from right side tool bar.
Draw a wire from the Pin 6 of the 6 Pin Connector to Pin 8 of the RTC
Select R1 and move to connect to the wire that was just created.
Select R2 and move to connect to the wire that was just created.
Select Place Symbol and then type VCC in pop up search window and click on OK. . 
Place just above the wire as seen in picture below

Connecting the Clock Crystal

Select Global Label right side tool bar and type OSCO in the text field.
Rotate and connect to Pin 2 of RTC. 
Hover over label and hit C key to Copy the label and then connect the copy to Pin 2 of the Crystal.
Select Global Label and type OSC in the text field. Rotate and connect to Pin 1 of RTC. 
Hover over label and hit C key to Copy the label and then connect the copy to Pin 1 of the Crystal.
As seen in picture below

Connecting I2C SDA & SCL

Select Place Wire from right side tool bar.
Draw a wire from the Pin 4 of the 6 Pin Connector to SCL Pin 6 of the RTC 
Draw a wire from the Pin 3 of the 6 Pin Connector to SDA Pin 5 of the RTC
Draw a wire from the bottom R1 and connect to the wire running from Pin 4 to PIN 6 (SCL) of the RTC
Draw a wire from the bottom R2 and connect to the wire running from Pin 3 to PIN 5 (SDA) of the RTC
As seen in picture below

Connecting the INTA

Select Global Label right side tool bar and type INTA in the text field.
Rotate and connect to Pin 2 of the 6 Pin Connector. 
Hover over label and hit C key to Copy the label and then connect the copy to Pin 7 of the RTC.
Select and Move R3 to connect bottom between the new label INTA and Pin 7 on the RTC.
Hover over the VCC symbol and hit C key to Copy the VCC symbol and then connect the VCC symbol to the 
top of R3
As seen in Figure below.

Finishing up and adding the Ground

Select Place Symbol and then type GND in pop up search window and click on OK. 
Connect GND symbol to Pin 1 of the 6 Pin connector. 
Select Place Wire from right side tool bar.
Draw wire from Pin 1 on 6 pin connector to Pin 4 on RTC. 
Hover over the GND symbol and hit C key to Copy the GND symbol 
Select r to rotate the symbol and connect to Pin 5 of the 6 Pin connector.
Hover over the GND symbol and hit C key to Copy the GND symbol again.
Connect GND to bottom of C1 
Hover over the VCC symbol and hit C key to Copy the VCC symbol 
Connect the VCC symbol to the top of C1

Connecting the optional Battery

Hover over the GND symbol and hit C key to Copy the GND symbol again.
Connect GND to bottom of C2 
Select Global Label right side tool bar and type VBAT in the text field.
Rotate and connect label to Pin 3 of the RTC.
Hover over the VBAT label and hit C key to Copy the VBAT label
Connect VBAT label to top of C2

Generate Netlist
1. From Schematic Layout Editor 
2. Select from Top Toolbar Generate Netlist 
3. From Popup select Generate Netlist 
4. Select Save

Now lets position the Component layout on PCB  

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